Methods for Isolation, Identification, and Quantification of miRNAs

ABSTRACT

Method and compositions and kits for isolation, identification, and quantification of miRNAs and other small RNAs, including but not limited to, siRNAs, mRNAs, and snRNAs are disclosed. Methods of diagnosing a disease or its progression are also disclosed.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a division of U.S. Nonprovisional patent applicationSer. No. 15/682,103, filed Aug. 21, 2017, which is a division of U.S.Nonprovisional patent application Ser. No. 13/350,277, filed Jan. 13,2012, now, abandoned, which claims the benefit of priority under 35U.S.C. § 119(e) to U.S. Provisional Patent Application No. 61/432,874,filed 14 Jan. 2011, which are herein incorporated by reference in theirentirety.

FIELD OF THE INVENTION

This application relates to method and compositions and kits forisolation, identification, and quantification of miRNAs and other RNAs,including but not limited to, siRNAs, mRNAs, and snRNAs.

BACKGROUND

MicroRNAs regulate virtually every aspect of biology, includingdevelopmental timing, differentiation, proliferation, antiviral defenseand metabolism, MicroRNAs are ^(˜)22-nucleotide-long RNAs that aregenerated by sequential processing from longer transcripts that containa stem-loop. One strand is loaded into the miRNA-induced silencingcomplex (miRISC), which contains the proteins argonaute (Ago) and Tnrc6(trinucleotide repeat-containing 6; GW182). The other strand is usuallydegraded. The mature miRNA guides the miRISC to partially complementarysequences, termed miRNA recognition elements (MREs), in target mRNAs torepress miRNA translation, promote transcript decay or both, MicroRNAsprobably regulate the expression of most coding genes. miRNAs have beenreported from all living organisms, including humans, bacteria, viruses,plants, worms, and others. About 3% of human genes encode for miRNAs andabout 30% of genes are believed to be regulated by miRNAs. It has alsobeen widely reported that an abnormal level of miRNA expression orpresence is associated with diseases, such as cancer, heart attack,diabetes, etc.

Quantitative and qualitative isolation of miRNAs from various biologicalsamples has been hampered for several reasons, including, but notlimited to, labor-intensive and time consuming protocols; the nature ofsmall size of miRNA leads to easy loss of the targets during extraction;miRNAs, like other RNAs, are not stable and can be degraded easilyduring processing and storage; the miRNA detection rate from realpatient samples is usually low or undetectable, i.e., not quantitative;and further the extracted miRNA targets normally are poorly correlatedbetween related study objects (e.g. placenta vs. blood).

For example, most miRNA (or RNA), isolation reagents or kits that arecommercially available (from QIAGEN-PAXGENE blood RNA kit,AMBION-LEUKOLOCK total RNA kit, and others), suffer from one or more ofthe following drawbacks: low sensitivity and detectability; low yield;not reproducible; large sample volume requirement; miRNA extraction doesnot scale well; time-consuming workflows, 4-5 hours workflow in general;low throughput and not automatable. Thus, there is a need in the fieldfor better methods for isolating, identifying, and quantifying miRNAs.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: Schematic for making anti-miRNA probe beads using chemicalsynthesis. Exemplary sequence shown in figure is AACTATACAACCTACTACCTCA(SEQ ID NO:1).

FIG. 2: Schematic for enzymatic synthesis of anti-miRNA probe beads.Exemplary sequence shown in figure is GCGGAGGGAAGCTCATCAG (SEQ ID NO:3).

FIG. 3A: Non-anti-probe beads hybridization with Cy3-labeled Let-7a.

FIG. 3B: Anti-Let-7a-probe beads hybridization with Cy3-labeled Let-7a.

FIG. 3C: FACS after de-hybridization of Cy3-labeled Let-7a bond fromanti-Let-7a-probe beads.

FIG. 4: Let-7 family miRNA profiling by C_(t) values.

FIG. 5: miRNA detection after addition (spiking) to plasma.

FIG. 6A: Quantitative real-time PCR Ct profiles of 96 miRNAs from blood.

FIG. 6B: Quantitative real-time PCR Ct profiles of 95 miRNAs from blood.

FIG. 7: Saliva miRNA profiling using anti-miRNA probe beads.

FIG. 8: A384C6 Beads showing Sensitivity and Dynamic Range of anti-miRNAprobe beads.

FIG. 9: miRNA Detectability and reproducibility.

FIG. 10A: Let7a-miRNA profiling from human bladder LCM samples; LCM areaand Ct correlation.

FIG. 10B: Let7c-miRNA profiling from human bladder LCM samples; LCM areaand Ct correlation.

FIG. 10C: miR-16-miRNA profiling from human bladder LCM samples; LCMarea and Ct correlation.

FIG. 11: Breast cancer FFPE sample miRNA profiling.

FIG. 12: Difference in expression of miRNA levels between breast cancerlines: MBA-MB-21 versus MCF-7 (delta Ct is shown).

FIG. 13: miRNA profiling from raw cow milk.

FIG. 14: miRNA profiling from urine from three donors.

FIG. 15: Megaplex A miRNA profiling from 25 microL serum.

FIG. 16: Megaplex B miRNA profiling from 25 microL serum.

FIG. 17: miRNA expression before and at 15-week of pregnancy.

SUMMARY OF THE INVENTION

As described above, the isolation, detection and quantification ofmiRNAs have been a daunting problem. Applicants have now developed asimple and elegant solution to the problem. In one embodiment, theinvention relates to a method for isolating, identifying, or quantifyingan miRNA from a sample of interest, comprising: contacting the sample ofinterest with an anti-miRNA probe covalently attached to a bead;incubating the sample of interest—bead mixture under suitable conditionsto form hybridized complexes between the miRNA in the sample of interestand the anti-miRNA probes on the beads; washing the beads under suitableconditions to remove the unbound sample material; and isolating,identifying, or quantifying the miRNA bound to the anti-miRNA probes.

In a further embodiment of the invention, the miRNA is isolated from theanti-miRNA probe beads before identifying or quantifying the miRNA.

In another embodiment of the invention, the identifying or quantifyingthe miRNA is comprises using reverse transcription followed byconventional or real-time or quantitative polymerase chain reaction(q-PCR) or other methods of amplification. In another embodiment, theidentifying or quantifying a miRNA involves non-qPCR techniques.

In one embodiment of the invention, the beads are magnetic beads. Inanother embodiment of the invention, the beads are non-magnetic beads.In one embodiment of the invention, the beads are carboxylic acidfunctionalized beads. In another embodiment of the invention, the beadsare DNA beads. In another embodiment of the invention, the beads are P1DNA beads.

In one embodiment of the invention, the anti-miRNA probe is attached tothe beads using chemical synthesis.

In another embodiment of the invention, the anti-miRNA probe is attachedto the beads using enzymatic synthesis. In another embodiment of theinvention, the enzymatic synthesis comprises: taking an oligonucleotidethat has a sequence complementary to an miRNA of interest (anti-miRNAprobe); adding a terminal didexoy nucleotide to the 3′ end using aterminal transferase; adding a 5′-phosphate group to the oligonucleotideusing a kinase; and ligating the oligonucleotide to DNA beads using asingle-strand DNA ligase. In one embodiment, the kinase is a T4polynucleotide kinase.

In one embodiment of the invention, a single species of ant-miRNA probeis attached to an individual bead. In another embodiment of theinvention more than one species of anti-miRNA probes are attached to anindividual bead.

In one embodiment of the invention, sample of interest is a biologicalsample. In another embodiment of the invention, the biological sample isselected from the group consisting of blood, serum, plasma, urine,saliva, cerebrospinal fluid, wound exudates, biopsies, autopsies,tissues, formalin-fixed, paraffin-embedded (FFPE) samples, or organs. Inanother embodiment of the invention, the biological sample is abiological fluid. In another embodiment of the invention, the biologicalfluid is blood. In another embodiment of the invention, the biologicalfluid is plasma. In another embodiment of the invention, the biologicalfluid is serum. In another embodiment of the invention, the biologicalfluid is saliva. In another embodiment, the sample could be a fossil ora fossilized rock or sediment.

In another embodiment, a method of diagnosing a disease or diseaseprogression is disclosed, comprising: identifying a set of miRNA markersthat are differentially regulated during a causation or progression of adisease; isolating and measuring the levels of such miRNA markers from asuitable biological sample from a patient in need thereof, at differenttime points if necessary; and diagnosing the disease or its progressionover time in the patient.

In another embodiment of the invention, a kit for isolating,identifying, or quantifying an miRNA from a sample of interest isprovided, comprising:

beads comprising anti-miRNA probe molecules covalently attached thereto;a wash buffer; and an elution buffer.

In another embodiment of the kit an instruction leaflet may be includeddescribing the product and protocol to carry out the inventive method.

DETAILED DESCRIPTION OF THE INVENTION

It is to be understood that the particular methods, reaction mixtures,and/or systems described herein may vary. The terminology used herein isfor the purpose of describing particular embodiments only, and is notintended to be limiting. Further, unless defined otherwise, alltechnical and scientific terms used herein have the same meaning ascommonly understood by one of ordinary skill in the art to which thisinvention pertains. As used in this specification and the appendedclaims, the singular forms “a”, “an”, and “the” also include pluralreferents unless the context clearly provides otherwise. All numericalranges are intended to encompass each individual value within the rangeas if each were separately listed (e.g., 10-20 may include one or moreof 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 and/or 20). In terms ofconcentration ranges, these encompass fractional ranges, e.g., allvalues between 10-20, represents as if each were individually writtenout (e.g., 10.8, 11.5). The term “approximately”, when used to modify agroup of numerical values, is meant to apply to each value individuallyunless otherwise indicated.

An “amplicon” typically refers to a molecule made by copying ortranscribing another molecule, e.g., as occurs in transcription,cloning, and/or in a polymerase chain reaction (“PCR”) (e.g., stranddisplacement PCR amplification (SDA), duplex PCR amplification, etc.) orother nucleic acid amplification technique. Typically, an amplicon is acopy of a selected nucleic acid or a portion thereof (e.g., a templateor target nucleic acid) or is complementary thereto. The term“amplifying” or “amplification” in the context of nucleic acidstypically refers to the production of multiple copies of apolynucleotide, or a portion of the polynucleotide, typically startingfrom a small amount of the polynucleotide (e.g., a single polynucleotidemolecule), where the amplification products or amplicons are generallydetectable. Any of several methods may be used to amplify the targetnucleic acid from the sample. The term “amplifying” which typicallyrefers to an “exponential” increase in target nucleic acid is being usedherein to describe both linear and exponential increases in the numbersof a select target sequence of nucleic acid. The term “amplificationreaction mixture” refers to an aqueous solution comprising the variousreagents used to amplify a target nucleic acid. These include enzymes,aqueous buffers, salts, amplification primers, target nucleic acid, andnucleoside triphosphates. Depending upon the context, the mixture can beeither a complete or incomplete amplification reaction mixture. Themethod used to amplify the target nucleic acid may be any available toone of skill in the art. Any in vitro means for multiplying the copiesof a target sequence of nucleic acid may be utilized. These includelinear, logarithmic, and/or any other amplification method. Exemplarymethods include polymerase chain reaction (PCR; see, e.g., U.S. Pat.Nos. 4,683,202; 4,683,195; 4,965,188; and/or 5,035,996), isothermalprocedures (using one or more RNA polymerases (see, e.g., WO2006/081222), strand displacement (see, e.g., U.S. Pat. No. RE39007E),partial destruction of primer molecules (see, e.g., WO2006087574)),ligase chain reaction (LCR) (see, e.g., Wu, et al., Genomics 4: 560-569(1990) and/or Barany, et al. PNAS USA 88:189-193 (1991)), 013 RNAreplicase systems (see, e.g., WO/1994/016108), RNA transcription-basedsystems (e.g., TAS, 3SR), rolling circle amplification (RCA) (see, e.g.,U.S. Pat. No. 5,854,033; U.S. Pub. No. 2004/265897; Lizardi et al. Nat.Genet. 19: 225-232 (1998); and/or Banér et al. Nucleic Acid Res., 26:5073-5078 (1998)), and strand displacement amplification (SDA) (Little,et al. Clin Chem 45:777-784 (1999)), among others. Many systems aresuitable for use in amplifying target nucleic acids and are contemplatedherein as would be understood by one of skill in the art.

Any of several methods may be used to detect target nucleic acids usingvarious primers and/or probes. Many different reagents, systems, and/ordetectable labels may be used in the methods described herein. Theseinclude, for example, TaqMan® systems, detectable label-quencher systems(e.g., FRET, salicylate/DTPA ligand systems (see, e.g., Oser et al.Angew. Chem. Int. Engl. 29(10):1167 (1990), displacement hybridization,homologous probes, assays described in EP 070685), molecular beacons(e.g., NASBA), Scorpion, locked nucleic acid (LNA) bases (Singh, et al.Chem Commun 4:455-456 (1998)), peptide nucleic acid (PNA) probes(Pellestor, et al. European J. Human Gen. 12:694-700 (2004)), Eclipseprobes (Afonina, et al. Biotechniques 32:940-949 (2002)), light-upprobes (Svanvik, et al. Anal Biochem 281:26-35 (2001)), molecularbeacons (Tyagi, et al. Nat. Biotechnol. 14:303-308 (1996)), tripartitemolecular beacons (Nutiu, et al. Nucleic Acids Res. 30:e94 (2002)),QuantiProbes (www.qiagen.com), HyBeacons (French, et al. Mol. Cell.Probes 15:363-374 (2001)), displacement probes (Li, et al. Nucleic AcidsRes. 30:e5 (2002)), HybProbes (Cardullo, et al. PNAS 85:8790-8794(1988)), MGB Alert (www.nanogen.com), Q-PNA (Fiandaca, et al. GenomeRes. 11:609-611 (2001)), Plexor (www.Promega.com), LUX primers(Nazarenko, et al. Nucleic Acids Res. 30:e37 (2002)), Scorpion primers(Whitcombe, et al. Nat Biotechnol 17:804-807 (1999)), AmpliFluor(Sunrise) primers (Nazarenko, et al. Nucleic Acids Res. 25:2516-2521(1997)), DzyNA primers (Todd, et al. Clin. Chem. 46:625-630 (2000)), andthe like. In each of these assays, the generation of amplificationproducts may be monitored while the reaction is in progress. Anapparatus for detecting the signal generated by the detectable label maybe used to detect, measure, and quantify the signal before, during,and/or after amplification. The particular type of signal may dictatethe choice of detection method. For example, in some embodiments,fluorescent dyes are used to label probes and/or amplified products. Theprobes bind to single-stranded and/or double-stranded amplifiedproducts, and/or the dyes intercalate into the double-stranded amplifiedproducts, and consequently, the resulting fluorescence increases as theamount of amplified product increases. In some embodiments, the T_(m) isascertained by observing a fluorescence decrease as the double-strandedamplified product dissociates and the intercalating dye is releasedtherefrom. The amount of fluorescence may be quantitated using standardequipment such as a spectra-fluorometer, for example. The use of othermethods and/or reagents is also contemplated herein.

One exemplary method for amplifying and detecting target nucleic acidsis commercially available as TaqMan® (see, e.g., U.S. Pat. Nos.4,889,818; 5,079,352; 5,210,015; 5,436,134; 5,487,972; 5,658,751;5,210,015; 5,487,972; 5,538,848; 5,618,711; 5,677,152; 5,723,591;5,773,258; 5,789,224; 5,801,155; 5,804,375; 5,876,930; 5,994,056;6,030,787; 6,084,102; 6,127,155; 6,171,785; 6,214,979; 6,258,569;6,814,934; 6,821,727; 7,141,377; and/or 7,445,900). TaqMan® assays aretypically carried out by performing nucleic acid amplification on atarget polynucleotide using a nucleic acid polymerase having 5′-3′nuclease activity, a primer capable of hybridizing to said targetpolynucleotide, and an oligonucleotide probe capable of hybridizing tosaid target polynucleotide 3′ relative to said primer. Theoligonucleotide probe typically includes a detectable label (e.g., afluorescent reporter molecule) and a quencher molecule capable ofquenching the fluorescence of said reporter molecule. Typically, thedetectable label and quencher molecule are part of a single probe. Asamplification proceeds, the polymerase digests the probe to separate thedetectable label from the quencher molecule. The detectable label (e.g.,fluorescence) is monitored during the reaction, where detection of thelabel corresponds to the occurrence of nucleic acid amplification (e.g.,the higher the signal the greater the amount of amplification).Variations of TaqMan® assays (e.g., LNA™ spiked TaqMan® assay) are knownin the art and would be suitable for use in the methods describedherein.

Another exemplary system utilizes double-stranded probes in displacementhybridization methods (see, e.g., Morrison et al. Anal. Biochem.,18:231-244 (1989); and/or Li, et al. Nucleic Acids Res., 30(2,e5)(2002)). In such methods, the probe typically includes two complementaryoligonucleotides of different lengths where one includes a detectablelabel and the other includes a quencher molecule. When not bound to atarget nucleic acid, the quencher suppresses the signal from thedetectable label. The probe becomes detectable upon displacementhybridization with a target nucleic acid. Multiple probes may be used,each containing different detectable labels, such that multiple targetnucleic acids may be queried in a single reaction.

Additional exemplary methods for amplifying and detecting target nucleicacids involve “molecular beacons”, which are single-stranded hairpinshaped oligonucleotide probes. In the presence of the target sequence,the probe unfolds, binds and emits a signal (e.g., fluoresces). Amolecular beacon typically includes at least four components: 1) the“loop”, an 18-30 nucleotide region which is complementary to the targetsequence; 2) two 5-7 nucleotide “stems” found on either end of the loopand being complementary to one another; 3) at the 5′ end, a detectablelabel; and 4) at the 3′ end, a quencher dye that prevents the detectablelabel from emitting a single when the probe is in the closed loop shape(e.g., not bound to a target nucleic acid). Thus, in the presence of acomplementary target, the “stem” portion of the beacon separates outresulting in the probe hybridizing to the target. Other types ofmolecular beacons are also known and may be suitable for use in themethods described herein. Molecular beacons may be used in a variety ofassay systems. One such system is nucleic acid sequence-basedamplification (NASBA1, a single step isothermal process for amplifyingRNA to double stranded DNA without temperature cycling. A NASBA reactiontypically requires avian myeloblastosis virus reverse transcriptase(AMV-RT or AMV), T7 RNA polymerase, RNase H, and two oligonucleotideprimers. After amplification, the amplified target nucleic acid may bedetected using a molecular beacon. Other uses for molecular beacons areknown in the art and would be suitable for use in the methods describedherein.

The Scorpion system is another exemplary assay format that may be usedin the methods described herein. Scorpion primers are bi-functionalmolecules in which a primer is covalently linked to the probe, alongwith a detectable label (e.g., a fluorophore) and a quencher. In thepresence of a target nucleic acid, the detectable label and the quencherseparate which leads to an increase in signal emitted from thedetectable label. Typically, a primer used in the amplification reactionincludes a probe element at the 5′ end along with a “PCR blocker”element (e.g., HEG monomer) at the start of the hairpin loop. The probetypically includes a self-complementary stem sequence with a detectablelabel at one end and a quencher at the other. In the initialamplification cycles (e.g., PCR), the primer hybridizes to the targetand extension occurs due to the action of polymerase. The Scorpionsystem may be used to examine and identify point mutations usingmultiple probes that may be differently tagged to distinguish betweenthe probes. Using PCR as an example, after one extension cycle iscomplete, the newly synthesized target region will be attached to thesame strand as the probe. Following the second cycle of denaturation andannealing, the probe and the target hybridize. The hairpin sequence thenhybridizes to a part of the newly produced PCR product. This results inthe separation of the detectable label from the quencher and causesemission of the signal. Other uses for molecular beacons are known inthe art and would be suitable for use in the methods described herein.

One or more detectable labels and/or quenching agents are typicallyattached to an oligonucleotide primer and/or probe. The detectable labelmay emit a signal when free or when bound to the target nucleic acid.The detectable label may also emit a signal when in proximity to anotherdetectable label. Detectable labels may also be used with quenchermolecules such that the signal is only detectable when not insufficiently close proximity to the quencher molecule. For instance, insome embodiments, the assay system may cause the detectable label to beliberated from the quenching molecule. Any of several detectable labelsmay be used to label the primers and probes used in the methodsdescribed herein. As mentioned above, in some embodiments the detectablelabel may be attached to a probe, which may be incorporated into aprimer, or may otherwise bind to amplified target nucleic acid (e.g., adetectable nucleic acid binding agent such as an intercalating ornon-intercalating dye). When using more than one detectable label, eachshould differ in their spectral properties such that the labels may bedistinguished from each other, or such that together the detectablelabels emit a signal that is not emitted by either detectable labelalone. Exemplary detectable labels include, for instance, a fluorescentdye or fluorophore (e.g., a chemical group that can be excited by lightto emit fluorescence or phosphorescence), “acceptor dyes” capable ofquenching a fluorescent signal from a fluorescent donor dye, and thelike. Suitable detectable labels may include, for example, fluorosceins(e.g., 5-carboxy-2,7-dichlorofluorescein; 5-Carboxyfluorescein (5-FAM);5-HAT (Hydroxy Tryptamine); 5-Hydroxy Tryptamine (HAT); 6-JOE;6-carboxyfluorescein (6-FAM); FITC); Alexa fluors (e.g., 350, 405, 430,488, 500, 514, 532, 546, 555, 568, 594, 610, 633, 635, 647, 660, 680,700, 750); BODIPY fluorophores (e.g., 492/515, 493/503, 500/510,505/515, 530/550, 542/563, 558/568, 564/570, 576/589, 581/591,630/650-X, 650/665-X, 665/676, FL, FL ATP, FI-Ceramide, R6G SE, TMR,TMR-X conjugate, TMR-X, SE, TR, TR ATP, TR-X SE), coumarins (e.g.,7-amino-4-methylcoumarin, AMC, AMCA, AMCA-S, AMCA-X, ABQ, CPMmethylcoumarin, coumarin phalloidin, hydroxycoumarin, CMFDA,methoxycoumarin), calcein, calcein AM, calcein blue, calcium dyes (e.g.,calcium crimson, calcium green, calcium orange, calcofluor white),Cascade Blue, Cascade Yellow; Cy™ dyes (e.g., 3, 3.18, 3.5, 5, 5.18,5.5, 7), cyan GFP, cyclic AMP Fluorosensor (FiCRhR), fluorescentproteins (e.g., green fluorescent protein (e.g., GFP. EGFP), bluefluorescent protein (e.g., BFP, EBFP, EBFP2, Azurite, mKalama1), cyanfluorescent protein (e.g., ECFP, Cerulean, CyPet), yellow fluorescentprotein (e.g., YFP, Citrine, Venus, YPet), FRET donor/acceptor pairs(e.g., fluorescein/tetramethylrhodamine, IAEDANS/fluorescein,EDANS/dabcyl, fluorescein/fluorescein, BODIPY FL/BODIPY FL,Fluorescein/QSY7 and QSY9), LysoTracker and LysoSensor (e.g.,LysoTracker Blue DND-22, LysoTracker Blue-White DPX, LysoTracker YellowHCK-123, LysoTracker Green DND-26, LysoTracker Red DND-99, LysoSensorBlue DND-167, LysoSensor Green DND-189, LysoSensor Green DND-153,LysoSensor Yellow/Blue DND-160, LysoSensor Yellow/Blue 10,000 MWdextran), Oregon Green (e.g., 488, 488-X, 500, 514); rhodamines (e.g.,110, 123, B, B 200, BB, BG, B extra, 5-carboxytetramethylrhodamine(5-TAMRA), 5 GLD, 6-Carboxyrhodamine 6G, Lissamine, Lissamine RhodamineB, Phallicidine, Phalloidine, Red, Rhod-2, 5-ROX (carboxy-X-rhodamine),Sulphorhodamine B can C, Sulphorhodamine G Extra, Tetramethylrhodamine(TRITC), WT), Texas Red, Texas Red-X, VIC and other labels described in,e.g., US Pub. No. 2009/0197254), among others as would be known to thoseof skill in the art. Other detectable labels may also be used (see,e.g., US Pub. No. 2009/0197254), as would be known to those of skill inthe art.

Nucleic acid binding agents may also be used to detect nucleic acidsamplified using the methods described herein. Many suitable detectablenucleic acid binding agents are available to one of skill in the art andmay be used alone or in combination with other agents and/or componentsof an assay system. Exemplary DNA binding agents may include, forexample, acridines (e.g., acridine orange, acriflavine), actinomycin D(Jain, et al. J. Mol. Biol. 68:21 (1972)), anthramycin, BOBO™-1,BOBO™-3, BO-PRO™-1, cbromomycin, DAPI (Kapuseinski, et al. Nuc. AcidsRes. 6(112): 3519 (1979)), daunomycin, distamycin (e.g., distamycin D),dyes described in U.S. Pat. No. 7,387,887, ellipticine, ethidium salts(e.g., ethidium bromide), fluorcoumanin, fluorescent intercalators asdescribed in U.S. Pat. No. 4,257,774, GelStar® (Cambrex Bio ScienceRockland Inc., Rockland, Me.), Hoechst 33258 (Searle and Embrey, 1990,Nuc. Acids Res. 18:3753-3762), Hoechst 33342, homidium, JO-PRO™-1, LIZdyes, LO-PRO™-1, mepacrine, mithramycin, NED dyes, netropsin,4′6-diamidino-α-phenylindole, proflavine, POPO™-1, POPO™-3, PO-PRO™-1,propidium iodide, ruthenium polypyridyls, S5, SYBR® Gold, SYBR® Green I(U.S. Pat. Nos. 5,436,134 and 5,658,751), SYBR® Green II, SYTOX blue,SYTOX green, SYTO® 43, SYTO® 44, SYTO® 45, SYTOX® Blue, TO-PRO®-1, SYTO®11, SYTO® 13, SYTO® 15, SYTO® 16, SYTO® 20, SYTO® 23, thiazole orange(Aldrich Chemical Co., Milwaukee, Wis.), TOTO™-3, YO-PRO®-1, and YOYO®-3(Molecular Probes, Inc., Eugene, Oreg.), among others. SYBR® Green I(see, e.g., U.S. Pat. Nos. 5,436,134; 5,658,751; and/or 6,569,927), forexample, has been used to monitor a PCR reaction by amplifying thetarget sequence in the presence of the dye, exciting the biologicalsample with light at a wavelength absorbed by the dye and detecting theemission therefrom; and, determining a melting profile of the amplifiedtarget sequence. The presence of amplified products and, therefore, thetarget sequence in the sample, may thereafter be determined by, forexample, performing a melting curve analysis (e.g., non-linear leastsquares regression of the sum of multiple gaussians). It is to beunderstood that the use of the SYBR® Green dye is presented as anexample and that many such dyes may be used in the methods describedherein. Other nucleic acid binding agents may also be suitable as wouldbe understood by one of skill in the art.

Nucleic acids “hybridize” or “anneal” in a base-pairing interaction ofone polynucleotide with another polynucleotide (typically anantiparallel polynucleotide) that results in formation of a duplex orother higher-ordered structure, typically termed a hybridizationcomplex. The primary interaction between the antiparallelpolynucleotides is typically base specific, e.g., A/T and G/C, byWatson/Crick and/or Hoogsteen-type interactions. It is not a requirementthat two polynucleotides have 100% complementarity over their fulllength to achieve hybridization. In some aspects, a hybridizationcomplex can form from intermolecular interactions, or alternatively, canform from intramolecular interactions. Hybridization occurs due to avariety of well-characterized forces, including hydrogen bonding,solvent exclusion, and base stacking. An extensive guide to nucleichybridization may be found in, Laboratory Techniques in Biochemistry andMolecular Biology-Hybridization with Nucleic Acid Probes, part I,chapter 2, “Overview of principles of hybridization and the strategy ofnucleic acid probe assays,” Elsevier (1993).

A “mixture” refers to a combination of two or more different components.A “reaction mixture” refers a mixture that comprises molecules that canparticipate in and/or facilitate a given reaction or assay. Toillustrate, an amplification reaction mixture generally includes asolution containing reagents necessary to carry out an amplificationreaction, and typically contains primers, a biocatalyst (e.g., a nucleicacid polymerase, a ligase, etc.), dNTPs, and a divalent metal cation ina suitable buffer. A reaction mixture is referred to as complete if itcontains all reagents necessary to carry out the reaction, andincomplete if it contains only a subset of the necessary reagents. Itwill be understood by one of skill in the art that reaction componentsare routinely stored as separate solutions, each containing a subset ofthe total components, for reasons of convenience, storage stability, orto allow for application-dependent adjustment of the componentconcentrations, and that reaction components are combined prior to thereaction to create a complete reaction mixture. Furthermore, it will beunderstood by one of skill in the art that reaction components arepackaged separately for commercialization and that useful commercialkits may contain any subset of the reaction or assay components, whichincludes the biomolecules of the invention.

A “moiety” or “group” refers to one of the portions into whichsomething, such as a molecule, is or can be divided (e.g., a functionalgroup, substituent group, or the like). For example, an oligonucleotidedescribed herein includes at least one donor moiety and/or at least oneacceptor moiety in certain embodiments.

The term “mutation” refers to a nucleic acid that has been altered inits nucleic acid sequence or an encoded protein product of a nucleicacid that has been altered in its amino acid sequence relative to anunaltered or native form of the nucleic acid or encoded protein product.Such alterations include, for example, point mutations or substitutions,deletions and insertions.

The term “nucleic acid” or “polynucleotide” refers to a polymer that canbe corresponded to a ribose nucleic acid (RNA) or deoxyribose nucleicacid (DNA) polymer, or an analog thereof. This includes polymers ofnucleotides such as RNA and DNA, as well as modified forms thereof,peptide nucleic acids (PNAs), locked nucleic acids (LNA™), and the like.In certain embodiments, a nucleic acid can be a polymer that includesmultiple monomer types, e.g., both RNA and DNA subunits. A nucleic acidcan be or can include, e.g., a chromosome or chromosomal segment, avector (e.g., an expression vector), an expression cassette, a naked DNAor RNA polymer, the product of a polymerase chain reaction (PCR), anoligonucleotide, a probe, a primer, etc. A nucleic acid may be, e.g.,single-stranded, double-stranded, triple-stranded (and the like) and isnot limited to any particular length. Unless otherwise indicated, aparticular nucleic acid sequence optionally comprises or encodescomplementary sequences, in addition to any sequence explicitlyindicated.

Nucleic acids are not limited to molecules having naturally occurringpolynucleotide sequences or structures, naturally occurring backbones,and/or naturally occurring internucleotide linkages. For example,nucleic acids containing one or more carbocyclic sugars are alsoincluded within this definition (Jenkins et al. (1995) Chem. Soc. Rev.pp 169-176, which is incorporated by reference). To further illustrate,although a nucleic acid will generally contain phosphodiester bonds, insome cases nucleic acid analogs are included that have alternatebackbones. These may include, without limitation, phosphoramide(Beaucage et al. (1993) Tetrahedron 49(10): 1925 and the referencestherein; Letsinger (1970) J. Org. Chem. 35:3800; Sprinzl et al. (1977)Eur. J. Biochem. 81:579; Letsinger et al. (1986) Nucl. Acids Res. 14:3487; Sawai et al. (1984) Chem. Lett. 805; Letsinger et al. (1988) J.Am. Chem. Soc. 110:4470; and Pauwels et al. (1986) Chemica Scripta26:1419), phosphorothioate (Mag et al. (1991) Nucleic Acids Res. 19:1437and U.S. Pat. No. 5,644,048), phosphorodithioate (Brill et al. (1989) J.Am. Chem. Soc. 111:2321), O-methylphophoroamidite linkages (Eckstein,Oligonucleotides and Analogues: A Practical Approach, Oxford UniversityPress (1992)), and peptide nucleic acid backbones and linkages (Egholm(1992) J. Am. Chem. Soc. 114:1895; Meier et al. (1992) Chem. Int. Ed.Engl. 31:1008; Nielsen (1993) Nature 365:566; and Carlsson et al. (1996)Nature 380:207). Other analog nucleic acids include those withpositively charged backbones (Denpcy et al. (1995) Proc. Natl. Acad.Sci. USA 92:6097); non-ionic backbones (U.S. Pat. Nos. 5,386,023,5,637,684, 5,602,240, 5,216,141 and 4,469,863; Angew (1991) Chem. Intl.Ed. English 30: 423; Letsinger et al. (1988) J. Am. Chem. Soc. 110:4470;Letsinger et al. (1994) Nucleoside & Nucleotide 13:1597; Chapters 2 and3, ASC Symposium Series 580, “Carbohydrate Modifications in AntisenseResearch”, Ed. Y. S. Sanghvi and P. Dan Cook; Mesmaeker et al. (1994)Bioorganic & Medicinal Chem. Lett. 4: 395; Jeffs et al. (1994) J.Biomolecular NMR 34:17; Tetrahedron Lett. 37:743 (1996)) and non-ribosebackbones, including those described in U.S. Pat. Nos. 5,235,033 and5,034,506, and Chapters 6 and 7, ASC Symposium Series 580, CarbohydrateModifications in Antisense Research, Ed. Y. S. Sanghvi and P. Dan Cook,which are each incorporated by reference. Several nucleic acid analogsare also described in, e.g., Rawls, C & E News Jun. 2, 1997 page 35.Modifications of the ribose-phosphate backbone may be done to facilitatethe addition of additional moieties, such as labeling moieties, or toalter the stability and half-life of such molecules in physiologicalenvironments.

In addition to naturally occurring heterocyclic bases that are typicallyfound in nucleic acids (e.g., adenine, guanine, thymine, cytosine, anduracil), nucleic acid analogs also include those having non-naturallyoccurring heterocyclic or other modified bases. For instance, certainbases used in nucleotides that act as melting temperature (T_(m))modifiers are optionally included. Exemplary of these are 7-deazapurines(e.g., 7-deazaguanine, 7-deazaadenine, and the like);pyrazolo[3,4-d]pyrimidines, propynyl-dN (e.g., propynyl-dU, propynyl-dC,and the like); hypoxanthine; inosine; xanthine; 8-aza derivatives of2-aminopurine, 2,6-diaminopurine, 2-amino-6-chloropurine, hypoxanthine,inosine and xanthine; 7-deaza-8-aza derivatives of adenine, guanine,2-aminopurine, 2,6-diaminopurine, 2-amino-6-chloropurine, hypoxanthine,inosine and xanthine; 6-azacytosine; 5-fluorocytosine; 5-chlorocytosine;5-iodocytosine; 5-bromocytosine; 5-methylcytosine; 5-propynylcytosine;5-bromovinyluracil; 5-fluorouracil; 5-chlorouracil; 5-iodouracil;5-bromouracil; 5-trifluoromethyluracil; 5-methoxymethyluracil;5-ethynyluracil; 5-propynyluracil; non-naturally occurring bases asdescribed by, for example, Seela et al. ((1991) Helv. Chim. Acta74:1790; (1999) Helv. Chim. Acta 82:1640); Grein et al. ((1994) Bioorg.Med. Chem. Lett. 4:971-976), U.S. Pat. Nos. 5,484,908, 5,645,985,5,990,303, 5,830,653, 6,639,059, 6,303,315, U.S. Pat. Appln. No.2003/0092905, and the like.

“Nucleoside” typically refers to a nucleic acid component that comprisesa base or basic group (e.g., comprising at least one homocyclic ring, atleast one heterocyclic ring, at least one aryl group, and/or the like)covalently linked to a sugar moiety (e.g., a ribose sugar, etc.), aderivative of a sugar moiety, or a functional equivalent of a sugarmoiety (e.g., an analog, such as carbocyclic ring). For example, when anucleoside includes a sugar moiety, the base is typically linked to a1′-position of that sugar moiety. As described above, a base can benaturally occurring (e.g., a purine base, such as adenine (A) or guanine(G), a pyrimidine base, such as thymine (T), cytosine (C), or uracil(U)), or non-naturally occurring (e.g., a 7-deazapurine base, apyrazolo[3,4-d]pyrimidine base, a propynyl-dN base, etc.). Exemplarynucleosides include ribonucleosides, deoxyribonucleosides,dideoxyribonucleosides, carbocyclic nucleosides, and the like. A“nucleotide” refers to an ester of a nucleoside, e.g., a phosphate esterof a nucleoside. To illustrate, a nucleotide can include 1, 2, 3, ormore phosphate groups covalently linked to a 5′ position of a sugarmoiety of the nucleoside. Nucleoside triphosphates and2′-deoxynucleoside triphosphates or their chemically modified versionsmay be used as substrates for multiple-nucleotide extension by APPwhere, for example, one nucleotide is incorporated the extending strandcan be further extended. 2′,3′-dideoxynucleoside triphosphates,chemically modified versions thereof, or other suitable compounds (e.g.,as in US 2005/0037398A1, acycloNMP) may be used as terminators forfurther extension may be used for single-nucleotide extension.2′,3′-dideoxynucleoside triphosphates may be labeled with radioactivityor fluorescence dye for differentiation from the 3′ terminaldideoxynucleotide of oligonucleotide P*. Mixtures of nucleosidetriphosphates or 2′-deoxynucleoside triphosphates and2′,3′-dideoxynucleoside triphosphates may also be used.

A “nucleotide incorporating biocatalyst” refers to a catalyst thatcatalyzes the incorporation of nucleotides into a nucleic acid.Nucleotide incorporating biocatalysts are typically enzymes. An “enzyme”is a protein- and/or nucleic acid-based catalyst that acts to reduce theactivation energy of a chemical reaction involving other compounds or“substrates.” A “nucleotide incorporating enzyme” refers to an enzymethat catalyzes the incorporation of nucleotides into a nucleic acid,e.g., during nucleic acid amplification or the like. Exemplarynucleotide incorporating enzymes include, e.g., polymerases, terminaltransferases, reverse transcriptases (e.g., RQY polymerase describedabove), telomerases, polynucleotide phosphorylases, and the like. A“thermostable enzyme” refers to an enzyme that is stable to heat, isheat resistant, and retains sufficient catalytic activity when subjectedto elevated temperatures for selected periods of time. For example, athermostable polymerase retains sufficient activity to effect subsequentprimer extension reactions when subjected to elevated temperatures forthe time necessary to effect denaturation of double-stranded nucleicacids. Heating conditions necessary for nucleic acid denaturation arewell known to persons skilled in the art and are exemplified in, forexample, U.S. Pat. Nos. 4,683,202, 4,683,195, and 4,965,188. To furtherillustrate, a “thermostable polymerase” refers to an enzyme that issuitable for use in a temperature cycling reaction, such as a polymerasechain reaction (“PCR”). For a thermostable polymerase, enzymaticactivity refers to the catalysis of the combination of the nucleotidesin the proper manner to form primer extension products that arecomplementary to a template nucleic acid. Exemplary thermostablepolymerases are described herein, and others may available to theskilled artisan may also be suitable.

TdT terminal deoxynucleotidyl transferase) catalyses the addition ofnucleotides to the 3′ terminus of a DNA molecule. Unlike most DNApolymerases it does not require a template. The preferred substrate ofthis enzyme is a 3′-overhang, but it can also add nucleotides to bluntor recessed 3′ ends. Cobalt is a necessary cofactor, however the enzymecatalyzes reaction upon Mg and Mn administration in vitro.

CircLigase™ (Epicentre Biotechnologies), ssDNA Ligase is a thermostableATP-dependent ligase that catalyzes intramolecular ligation (i.e.circularization) of ssDNA templates having a 5″-phosphate and a3″-hydroxyl group. In contrast to T4 DNA Ligase and Ampligase® DNALigase, which ligate DNA ends that are annealed adjacent to each otheron a complementary DNA sequence, CircLigase ssDNA Ligase ligates ends ofssDNA in the absence of a complementary sequence. The enzyme istherefore useful for making circular ssDNA molecules from linear ssDNA.Circular ssDNA molecules can be used as substrates for rolling-circlereplication or rolling-circle transcription. Linear ssDNA of >30 basesis circularized by CircLigase enzyme. Under standard reactionconditions, virtually no linear concatamers or circular concatamers areproduced. In addition to its activity on ssDNA, CircLigase enzyme alsohas activity in ligating a single-stranded nucleic acid having a3″-hydroxyl ribonucleotide and a 5″-phosphorylated ribonucleotide ordeoxyribonucleotide.

An “oligonucleotide” refers to a nucleic acid that includes at least twonucleic acid monomer units (e.g., nucleotides), typically more thanthree monomer units, and more typically greater than ten monomer units.The exact size of an oligonucleotide generally depends on variousfactors, including the ultimate function or use of the oligonucleotide.Typically, the nucleoside monomers are linked by phosphodiester bonds oranalogs thereof, including phosphorothioate, phosphorodithioate,phosphoroselenoate, phosphorodiselenoate, phosphoroanilothioate,phosphoranilidate, phosphoramidate, and the like, including associatedcounterions, e.g., H⁺, NH₄ ⁺, Na⁺, and the like, if such counterions arepresent. Typically, the 3′ end linkage of P* is a phosphodiester bond.Oligonucleotides may be prepared by any suitable method, including, butnot limited to, isolation of an existing or natural sequence, DNAreplication or amplification, reverse transcription, cloning andrestriction digestion of appropriate sequences, or direct chemicalsynthesis by a method such as the phosphotriester method of Narang etal. ((1979) Meth. Enzymol. 68:90-99); the phosphodiester method of Brownet al. ((1979) Meth. Enzymol. 68:109-151); the diethylphosphoramiditemethod of Beaucage et al. ((1981) Tetrahedron Lett. 22:1859-1862); thetriester method of Matteucci et al. ((1981) J. Am. Chem. Soc.103:3185-3191); automated synthesis methods; or the solid support methoddescribed in U.S. Pat. No. 4,458,066, and/or other methods known tothose skilled in the art.

A “primer nucleic acid” or “primer” is a nucleic acid that can hybridizeto a target or template nucleic acid and permit chain extension orelongation using, e.g., a nucleotide incorporating biocatalyst, such asa polymerase under appropriate reaction conditions. A primer nucleicacid is typically a natural or synthetic oligonucleotide (e.g., asingle-stranded oligodeoxyribonucleotide). Although other primer nucleicacid lengths are optionally utilized, they typically comprisehybridizing regions that range from about 8 to about 100 nucleotides inlength. Shorter primer nucleic acids generally require lowertemperatures to form sufficiently stable hybrid complexes with templatenucleic acids. A primer nucleic acid that is at least partiallycomplementary to a subsequence of a template nucleic acid is typicallysufficient to hybridize with the template for extension to occur. Aprimer nucleic acid may be labeled, if desired, by incorporating adetectable label as described herein.

The term “probe nucleic acid” or “probe” refers to a labeled orunlabeled oligonucleotide capable of selectively hybridizing to a targetor template nucleic acid under suitable conditions. Typically, a probeis sufficiently complementary to a specific target sequence contained ina nucleic acid sample to form a stable hybridization duplex with thetarget sequence under selected hybridization conditions. A hybridizationassay carried out using a probe under sufficiently stringenthybridization conditions permits the selective detection of a specifictarget sequence. The term “hybridizing region” refers to that region ofa nucleic acid that is exactly or substantially complementary to, andtherefore capable of hybridizing to, the target sequence. For use in ahybridization assay for the discrimination of single nucleotidedifferences in sequence, the hybridizing region is typically from about8 to about 100 nucleotides in length. Although the hybridizing regiongenerally refers to the entire oligonucleotide, the probe may includeadditional nucleotide sequences that function, for example, as linkerbinding sites to provide a site for attaching the probe sequence to asolid support. A probe of the invention may be generally included in anucleic acid that comprises one or more labels (e.g., donor moieties,acceptor moieties, and/or quencher moieties), such as a 5′-nucleaseprobe, a hybridization probe, a fluorescent resonance energy transfer(FRET) probe, a hairpin probe, or a molecular beacon, which can also beutilized to detect hybridization between the probe and target nucleicacids in a sample. In some embodiments, the hybridizing region of theprobe is completely complementary to the target sequence. However, ingeneral, complete complementarity is not necessary (e.g., nucleic acidscan be partially complementary to one another); stable hybridizationcomplexes may contain mismatched bases or unmatched bases. Modificationof the stringent conditions may be necessary to permit a stablehybridization complex with one or more base pair mismatches or unmatchedbases. Sambrook et al., Molecular Cloning: A Laboratory Manual, 3rd Ed.,Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2001)provides guidance for suitable modification. Stability of thetarget/probe hybridization complex depends on a number of variablesincluding length of the oligonucleotide, base composition and sequenceof the oligonucleotide, temperature, and ionic conditions. One of skillin the art will recognize that, in general, the exact complement of agiven probe is similarly useful as a probe. One of skill in the art willalso recognize that, in certain embodiments, probe nucleic acids canalso be used as primer nucleic acids.

The methods described herein may be useful for detecting and/orquantifying a variety of target nucleic acids from a test sample. Atarget nucleic acid is any nucleic acid for which an assay system isdesigned to identify or detect as present (or not), and/or quantify in atest sample. Such nucleic acids may include, for example, those ofinfectious agents (e.g., virus, bacteria, parasite, and the like), adisease process such as cancer, diabetes, or the like, or to measure animmune response. Exemplary “test samples” include various types ofsamples, such as biological samples. Exemplary biological samplesinclude, for instance, a bodily fluid (e.g., blood, saliva, or spinalfluid), a tissue sample, a food (e.g., meat) or beverage (e.g., milk)product, or the like. Expressed nucleic acids may include, for example,genes for which expression (or lack thereof) is associated with medicalconditions such as infectious disease (e.g., bacterial, viral, fungal,protozoal infections) or cancer. The methods described herein may alsobe used to detect contaminants (e.g., bacteria, virus, fungus, and/orprotozoan) in pharmaceutical, food, or beverage products. The methodsmay be useful to, for example, detect minimal residual disease (e.g.,rare remaining cancer cells during remission, especially mutations inthe p53 gene or other tumor suppressor genes previously identifiedwithin the tumors), and/or measure mutation load (e.g., the frequency ofspecific somatic mutations present in normal tissues, such as blood orurine).

Kits for performing the methods described herein are also provided. Thekit typically includes at least a pair of oligonucleotides (e.g., atleast one of the pair being a P* oligonucleotide) for amplifying atleast one target nucleic acid from a sample, one or morepolyphosphorolyzing agents described herein, a biocatalyst (e.g., DNApolymerase) and/or corresponding one or more probes labeled with adetectable label. The kit may also include samples containingpre-defined target nucleic acids to be used in control reactions. Thekit may also optionally include stock solutions, buffers, enzymes,detectable labels or reagents required for detection, tubes, membranes,and the like that may be used to complete the amplification reaction. Insome embodiments, multiple primer sets are included. Other embodimentsof particular systems and kits are also contemplated.

Magnetic polymer particles are of general utility in various medical andbiochemical fields, for example as transport vehicles for the deliveryof pharmaceutical products, for diagnostic purposes, for separation andfor synthetic purposes. Such particles rely upon their magneticproperties in order to perform these functions: in diagnostic assayapplications, for example, application of a magnetic field to a samplecontaining an analyte bound to magnetic polymer particles allows theisolation of the analyte without the use of centrifugation orfiltration; and in therapeutic applications, for example, application ofa magnetic field to the patient may serve to target drug-carryingmagnetic polymer particles to a desired body site.

By magnetic is meant herein that the polymer particles containsuperparamagnetic crystals. Thus the magnetic polymer particles aremagnetically displaceable but are not permanently magnetizable. Manyprocesses for preparing magnetic polymer particles are known, a largenumber of which involve preparing maghemite- or magnetite-containingpolymer particles from pre-formed magnetic iron oxides, e.g. magnetite.Some of processes involved are described in U.S. Pat. No. 4,654,267(Ugelstad).

The magnetic polymer particles used in the process of the invention maybe any magnetic polymer particle e.g. as described in U.S. Pat. No.4,654,267. The particles are preferably porous to allow the presence ofthe superparamagnetic crystals in the pores thereof. The surface of themagnetic particles is normally functionalized to allow coupling of aligand to the polymer particle, e.g. it may be functionalized to carryany known surface structure such as carboxyl groups, tosyl groups, aminogroups, epoxy groups, maleamido groups, thiol groups etc. Hence, thesurface may be amine functionalized. Alternatively, an aminefunctionalized surface can itself be further functionalized to carryother functional groups, e.g. COOH groups.

The polymer particle is preferably made from combinations of vinylicpolymers (e.g. styrene), acrylates and/or methacrylates. The polymericmaterial may optionally be cross-linked, for example by incorporation ofcross-linking agents, for example as comonomers, e.g. divinylbenzene(DVB) or ethyleneglycol dimethacrylate. Appropriate quantities of thecross-linking agents (e.g. comonomers) required will be well known tothe skilled person. Preferably the polymer is a cross-linked styrenicpolymer (e.g. a styrene-divinylbenzene polymer, surface functionalizedby the use of a nitro-group containing comonomer, e.g. nitro-styrene,and subsequent reduction) or a cross-linked (meth)acrylic polymersurface functionalized by the use of an epoxy-group containingco-monomer (e.g. glycidylmethacrylate) and subsequent amination (e.g. byreaction with ethylene diamine).

The superparamagnetic crystals in the polymer particles used in theprocess of the invention may be of any material capable of beingdeposited in superparamagnetic crystalline form in the porous polymerparticles. Magnetic iron oxides, e.g. magnetite or maghemite arepreferred; however the crystals may be of mixed metal oxides or othermagnetic material if desired. The total quantity of crystalline magneticmaterial present is generally more than 1%, preferably more than 3%,desirably more than or equal to 5% (by weight, e.g. up to 40% wt. Thepercentage is calculated on a Fe (or equivalent metal in the case ofmagnetic materials other than iron oxides) weight basis based upon theoverall dry weight of the coated particles.

Polymer particles according to the various aspects of the presentinvention may generally have sizes (i.e. diameters) that are in themicrometer range, e.g. 0.3 to 100 μm, especially 0.5 to 50 μm, moreespecially 0.8 to 8 μm, e.g. 0.8 to 1.2 μm. 1 μm beads are referred.

Typically the porous particles used will have a surface area of at least15 m²/g (measured by the BET nitrogen absorption method), and morepreferably at least 30 m²/g, e.g. up to 700 m²/g, when corrected to amean particle diameter of 2.7 μm (i.e. multiply surface area by 2.7/MD,where MD is the mean diameter in micrometers). Similarly scaled, theparticle pore volume is preferably at least 0.1 mL/g.

Typically, the polymer particles are spherical and substantiallymonodisperse before they are coated and especially preferably remainspherical and substantially monodisperse once they have been coated.

By substantially monodisperse, it is meant that for a majority ofparticles, the particles have a coefficient of variation (CV) of lessthan 20%, for example less than 15%, preferably less than 12%, morepreferably less than 11%, still more preferably less than 10% and mostpreferably no more than about 8%, e.g. 2 to 5%. CV is determined inpercentage as CV=(100×standard deviation)/mean where mean is the meanparticle diameter and standard deviation is the standard deviation inparticle size. CV is preferably calculated on the main mode, i.e. byfitting a monomodal distribution curve to the detected particle sizedistribution. Thus some particles below or above mode size may bediscounted in the calculation which may for example be based on about90% of total particle number (of detectable particles that is). Such adetermination of CV may be performable on a Coulter or other particlesize analyzer.

Functionalization of the polymeric material may take place afterpolymerization by, for example, nitration and subsequent reduction ofthe thus-formed nitro groups to pendant amine groups; or directamination, for example by treatment with amino ethanol. As furtheralternatives, polymeric particles prepared by the well-known Ugelstadtwo-step swelling process and the improvements thereto disclosed in WO00/61647 may be used. Porous polymer particles produced according to theprocesses described in this publication may have magnetic particlesdeposited in their pores by standard techniques.

As a further possibility, porous polymer particles may be prepared fromnitro styrene and DVB, and magnetic material introduced as taught inU.S. Pat. No. 4,654,267.

The superparamagnetic polymer beads sold by Life Technologies(Invitrogen Dynal Biotech ASA), under the trade names DYNABEADS,especially DYNABEADS MYONE are especially preferred. DYNABEADS areparticularly advantageous since they remain in suspension and do notexhibit magnetic particle sedimentation often associated with othermagnetic beads. DYNABEADS also show excellent magnetic mobility comparedto other magnetic particles in which high levels of iron are present.DYNABEADS exhibit beneficial kinetics allowing shorter reaction timesand higher throughputs. Their non-specific binding is lower than othermagnetic beads and their proper use results in a concentration of thedesired material taking place resulting in easier and more efficientwashing procedures. DYNABEADS MYONE beads are easy to automate and aremonodisperse. DYNABEADS MYONE carboxylic acid beads are used generally;however, other functional groups may also be utilized.

Certain embodiments are further described in the following examples.These embodiments are provided as examples only and are not intended tolimit the scope of the claims in any way. All references, including USpatents, patent applications, PCT applications and articles cited withinthis application are incorporated by reference in their entirety intothis application.

EXAMPLES Example 1

Covalent Bead—Anti-miRNA Probe Bead—Chemical Preparation.

Schematic is shown in FIG. 1.

Reagents: EDC, miRNA oligo, and MYONE beads (Beads: 1 mL=10 mg=10billion).

One ml of MYONE carboxylic acid beads (10 billion beads) are placed in1.5 ml microfuge tube. Beads are washed with 1000 μL 10 mM NaOH 3 times.Beads are further washed with 10000 μL deionized H₂O, 4 times. pH isadjusted to about 6.5-7. A reaction master mix is prepared in 1.5 mLtube, as follows:

add H₂O 80 μL add 20 μL 5M NaCl add 248 μL DMSO

1M EDC is prepared in 5 mM aqueous Imidazole-HCl. One mg/5.2 μL=18mg/100 μL 5 mM aqueous Imidazole is prepared. 192 μL (2×) of 0.5 mMaqueous anti-miRNA oligo is added to the master mix. Beads are suspendedin reaction master mix and treated as follows: remove the H₂O from thebeads

add 100 μL 1M EDC solution to the reaction master Mixadd the anti-miRNA oligo/Master Mix/EDC to the beadsimmediately vortex and sonicate 3 times.place the tube on a rotator.

The tube is rotated overnight at room temperature. The beads are furtherwashed as follows: Wash with 1000 μL DMSO. Wash 2 times with 1000 μLdeionized water. Wash 2 times with 1000 μL 1×TEX (Tris, EDTA, TritonX-100). Wash 3 times with 1000 μL 1×TEX and heat for 8 min at 80° C.Beads are stored in 1.00 mL 1×TEX at 4° C.

Example 2

Covalent Anti-miRNA Bead—Enzymatic Preparation

Schematic is shown in FIG. 2.

3′-Modification and 5′-Phosphorylation of anti-miRNA Probes

Reagents: Terminal Transferase, ddTTP (TriLink),

miRNA- Probe Sequence Tm Let-7aP 5′AACTATACAACCTACTACCTCA 46.41 (SEQ IDNO: 1) Let-7bP 5′AACCACACAACCTACTACCTCA 54.8 (SEQ ID NO: 2)

3′-Modification Procedure

Final Component Let-7aP Let-7bP Concentration 10X Terminal TransferaseBuffer 10 10 1X 10X Cobalt Chloride 10 10 1X 20 U/μL TerminalTransferase 10 10 0.4 U/μL 1 mM ddTTP 10 10 100 μM 5′P-Probe 30 30 ~20uM H₂O 30 30 Total 100 100 Input Yield Output 19.3 OD × 15.5 OD × 30 μL30 μL

The reaction is incubated at 37° C. for 2 hrs. The terminal transferaseis inactivated by heating the reaction mix at 95° C. for 5 min.

Phosphorylation Procedure

Component Let-7aPddT Let-7bPddT Carryover from above 100 100 10X KinaseBuffer 20 20 10 mM ATP 20 20 10 U/μL T4 Kinase 15 15 DI Water 45 45Total (μL) 200 200 Oligo Output (OD)  F3 1.5 × 50 μL  F3 2.7 × 50 μL F425.9 × 50 μL F4 26.9 × 50 μLThe reaction mix is incubated at 37° C. for 1 hr. Purification is doneusing PD-10 column by desalting.

Bead Ligation with 5T-Let-7a, b, c, d, e and f Probe-3′ ddT

Reagents: SOLID™ P1 DNA Beads (ABI), 5T-Let-7a, b, c, d, e and f Probes,Ligation Buffer (EpiCentre Biotechnologies), Ligase (EpiCentreBiotechnologies), ATP (Ambion), MnCl₂ (Teknova), PEG6000 (EmeraldBiosystems).

Stock Volume Final Concentration Component Concentration for 2X (μL)(1X) 10X Ligation Buffer 10X 160 1X 50% PEG6000 50% 240 7.5% 25 mM MnCl₂25 mM 160 2.5 mM 250 μM ATP 250 uM 160 25 μM H2O 80 Total 800

Pre-Treatment of Beads

Transferred 3004 beads (10 million/μL×50=500 million beads×6) to aLo-Bind tube. Placed the Lo-Bind tube in a magnetic rack for 1 min andremoved the supernatant. Added 200 μL 1×TEX (Tris-EDTA-Triton X-100)buffer. Sonicated the beads using Covaris Covalent Declump 1. Placed theLo-Bind tube in a magnetic rack for 1 min and remove the supernatant.Added 150 μL the Buffer mix and 150 μL H₂O. Vortexed. Divided the beadsinto 6 tubes, 50 μL each. Placed the Lo-Bind tubes in a magnetic rackfor 1 min and removed the supernatant.

Added Following Reaction Mix into the Tube: Ligation Reaction

Component 7a 7b 7c 7d 7e 7f Solid P1 Beads 500 500 500 500 500 500 (500million beads) million million million million million million 2X BufferMix 100 100 100 100 100 100 5′P-Let-7P-3′-ddT A260 11.8 A260 10.5 A2604.92 A260 4.44 A260 4.59 A260 4.55 A260 5′P-Let-7P-3′-ddT 40 40 80 80 8080 H₂O 40 40 0 0 0 0 100U/μL CircLigase I 20 20 20 20 20 20 Total 200200 200 200 200 200

Incubated Reaction Tubes at 60° C. Overnight on ThermoMixer at 1100 Rpm.

Bead Clean-Up:

Denaturing Solution: Added 200 μL Denaturant to 1800 μL, 1× Denaturingbuffer and mixed well. Placed the reaction tube in a magnetic rack for 1min and remove the supernatant. Added 200 μL 1×TEX buffer. Sonicated thebeads using Covaris Covalent Declump 1. Placed the tube in a magneticrack for 1 min and removed the supernatant. Added 200 μL of theDenaturing Buffer, vortexed, and let stand for 1 min. Placed the tube ina magnetic rack for 1 min and removed the supernatant. Added 200 μL1×TEX buffer, vortexed and pulsed down. Placed the tube in a magneticrack for 1 min and removed the supernatant. Repeat twice. Beads arestored (in 2004 TEX buffer, ^(˜)2.5 million beads/pi) at 4° C.

Example 3

Hybridization of Ant-miRNA Beads (Hybridization with Cy3-Labeled miRNA)

Fluorescent flow cytometry analysis is done to ensure that anti-miRNAprobes are covalently attached to the beads and that Cy3-labeled miRNAsare effectively captured by the anti-miRNA beads.

Reagents: Anti-ath-miR159 Beads, Cy-3-ath-miR159a, Control:non-anti-probe beads, Cy3-ath-miR159a.

Hybridization is Carried Out Using the Following Protocol:

Sonicate the beads with Covalent Declump 1 on Covaris. Aliquot 1 μL ofath-miR159a beads and 1 μL Solid P1beads into 1.5 mL LoBind tubesseparately. Add 1004 hybridization buffer. Add 5 μL 100 μMCy3-ath-miR159a and vortex. Shake tubes at 1200 rpm for 20 min at roomtemperature. Magnet the beads for 1 mins and remove the supernatant. Add2004 RNA Purification Wash Solution 1 (ABI). Vortex and incubate for 1min before placing tubes on magnetic rack. Magnet and after 1 min,remove the supernatant. Add 2004 RNA Purification Wash Solution 2 (ABI).Vortex and incubate for 1 min before placing tubes on magnetic rack. Add200 μL 0.5×SSPE/T buffer (ABI). Vortex and incubate for 1 min beforeplacing tubes on magnetic rack. Briefly spin the tubes, magnet, andafter 1 min, remove the supernatant. Add 100 μL 0.5×SSPE/T Buffer,vortex, and sonicate with an ultrasonic bath briefly. ABI is AppliedBioSystems, Inc. miRNAs may be eluted from the beads by de-hybridizationusing buffers that are known to one skilled in the art, e.g., 10 mMTris:HCl or 10 mM Tris:HCl with 01 mM EDTA.

Fluorescent Flow Cytometry (FACS) (BD Bioscience) Analysis

Add about 2504 FACS read buffer. Add 104 beads. Read. The beads arefluorescent and the center of the distribution peak of the beads isdistinctively different from the control beads. Representative FACSprofiles are shown in FIGS. 3A-3C.

Example 4

Let-7 miRNA Profiling from Red Blood Cells and Plasma

Reagents: P1-Let-7a-f Beads, Tempus Buffer (ABI), Finger Tip Fresh Blood

Blood Sample Collection: 40 μL of fresh finger blood sample wascollected in a tube containing 0.4 μL of 0.5M EDTA (pH 8.0) using a minifinger lancet.

Plasma and Red Blood Cells Separation and Lysis: The blood sample iscentrifuged and the plasma is carefully pipetted out. 204 plasma ismixed with 40 μL Tempus buffer. The red blood cells are washed with 100μL 0.9% NaCl, centrifuged, and the supernatant is removed. Washing isrepeated 2 more times. 10 μL red blood cells are mixed with 20 μL TempusBuffer.

Hyb Sample Serial Dilution: 6 μL of the lysate solution prepared aboveis diluted in 194 μL Oligo dT hybridization buffer and vortexed. This isHyb sample A (14 blood in 100 μL volume). The samples are seriallydiluted according to following table for the rest of Hyb samples.

Hyb Oligo dT Lys/ Sample and Total Volume, Blood, Sample Bind BufferVolume μL nL A 1000 B 135  A: 15 μL 150 100 C 135  B: 15 μL 150 10 D 135 C: 15 μL 150 1 E 135 D: 151 μL 150 0.1

Hybridization: 5 μL each of Let-7a thru Let-7f beads (^(˜)2.5million/μL, 12.5 million total each) are combined in a LoBind tube, 200μL TEX buffer is added, and the tubes are vortexed. Tubes/beads aremagnetized to remove the supernatant. 6 μL of the mixed beads are addedinto each hybridization sample as prepared above. The beads are shakenat 1100 rpm for 20 min at room temperature. The beads are magnetized toremove the supernatants. The beads are washed according to the followingtable. Finally, 1×TE buffer is added and the beads are sonicated withCovalent Declump 1.

Wash 1, Wash 2, Suspension, Test Beads 100 μL 100 μL 100 μL 1X TE ALet-7a-f Buffer A Buffer B 1X TE (0.125 million/μL) B Let-7a-f Buffer ABuffer B 1X TE (0.125 million/μL) C Let-7a-f Buffer A Buffer B 1X TE(0.125 million/μL) D Let-7a-f Buffer A Buffer B 1X TE (0.125 million/μL)E Let-7a-f Buffer A Buffer B 1X TE (0.125 million/μL)

Reverse Transcription (RT): The captured miRNAs (in suspension, aboveTable) are reverse transcribed to cDNA using TaqMan® MicroRNA ReverseTranscription Kit (ABI) following the recommended protocol. Thereactions are incubated at 16° C./30 min, 42° C./30 min, and 85° C./5min.

TaqMan PCR Reaction: The reverse-transcribed cDNA from the capturedmiRNAs are quantitatively analyzed using Applied Biosystems miRNA TaqManassays and TaqMan Universal PCR Master Mix following the recommendedprotocols. TaqMan real-time PCR reactions are run on Applied Biosystems7500 instrument using the default cycling parameters. The results arelisted in Table 1 and FIG. 4.

TABLE 1 (C_(t) values for each Let-7 species are shown) Blood VolumeLet-7a Let-7b Let-7c Let-7d Let-7e Let-7f NTC 40.00 40.00 40.00 40.0040.00 39.00   1 nL 33.21 32.89 34.48 36.17 39.03 34.34   10 nL 31.0130.99 36.54 32.01 36.08 34.33  100 nL 27.74 27.68 34.12 28.24 37.2830.27  1000 nL 24.25 24.52 31.46 25.19 35.32 27.92 10000 nL 21.78 21.0327.50 22.46 32.57 24.19 Linear Data Points 4 4 3 5 2 4 Slope 3.12 3.303.31 3.42 3.28 R2 0.99 0.99 0.99 0.99 0.99

Example 5: miRNA Spiking and Recovery Test from a Plasma Sample

A mixture of Let-7a-f miRNAs was spiked in plasma. The spiked plasmasample was serially diluted 10× with Hyb buffer. The miRNAs werecaptured and quantified by the beads and TaqMan PCR. Results are shownin FIG. 5.

Example 6

Capturing and Quantification of a Panel of 96 miRNAs Using Anti miRNABeads

The following protocol was used. Dilute 5 μL fresh blood in 490 μLHybridization Dilution buffer (ABI). Spike in 5 μL of 1 nM ath-miR159aRNA Artificial Template. Add anti miRNA beads prepared according toExample 2 with 96 anti miRNA oligonucleotides and shake at 1200 rpm for20 min at room temperature to hybridize. Wash the beads with RNAPurification Wash Solution I and RNA Purification Wash Solution II asdescribed previously. Add elution buffer and vortex to mix. Heat beadelution sample in 70° C. for 2 minutes and then place immediately onice. Perform reverse transcription and TaqMan real-time PCR as describedin Example 4. The quantitative real-time PCR Ct profiles are shown inFIG. 6A. A similar experiment is conducted on 50 microL of human plasma.The results are presented in FIG. 6B. miRNA detectability andreproducibility was further confirmed as shown in FIG. 9 and the tablebelow:

Run 1 Run 2 Total miRNA Tested 96 96 Detectable miRNA (Ct < 35) 71 70Undetectable miRNA 25 26 Detection Rate 74.0% 72.9%

Example 7

miRNA capturing and quantification from saliva. The following protocolwas used.

Collect about 200 μL saliva and centrifuge briefly. Take 100 μL of thecentrifuged saliva and add to 196 μL Hybridization buffer. Vortexvigorously for 30 seconds. Spike in 4 μL of 1 nM ath-miR159a RNAArtificial Template. This is Sample E. Dilute Sample E seriallyaccording to following table using Hybridization buffer.

Hyb Hyb Dilution Stock Sample Total Saliva Input Sample buffer μL andVolume Volume μL nL/100 μL E Prepared in step 1 33300 D 135 E: 15 μL 1503330 C 135 D: 15 μL 150 333 B 135 C: 15 μL 150 33.3 A 135 B: 15 μL 1503.33

Add anti miRNA beads to Hyb Samples A, B, C, D, and E prepared above.Shake the hybridization samples in tubes at 1200 rpm for 20 min at roomtemperature. Wash the beads with RNA Purification Wash Solution I andRNA Purification Wash Solution II as described previously. Add elutionbuffer and vortex to mix. Heat bead elution sample in 70° C. for 2minutes and then place immediately on ice. Perform reverse transcriptionand TaqMan real-time PCR as described in Example 4. The quantitativereal-time PCR Ct profiles are shown in table below and in FIG. 7.

Let-7a Let-7b Let-7c Let-7d Let-7e Let-7f ath-159a miR320 NTC 40.0036.58 37.30 40.00 40.00 40.00 37.13 40.00   3 nL 34.65 33.11 35.49 38.6040.00 37.15 29.54 34.09   30 nL 31.84 32.13 34.83 38.60 40.00 35.4327.25 34.24  300 nL 29.44 29.77 31.80 34.09 40.00 34.13 23.75 34.04 3000 nL 26.97 26.93 29.93 30.52 36.23 30.08 20.33 31.45 30000 nL 24.0324.07 26.96 27.67 33.80 27.50 17.04 28.66

Example 8 Protocols for miRNA Detection and Profiling Using Anti-ProbeBeads

Two anti-miRNA bead Panels: A384C6: beads with 386 miRNA targets basedon the ABI Megaplex A assay panel. B384C6: beads with 385 miRNA targetsbased on the ABI Megaplex B assay panel.

None-Human miRNA Controls: Each panel contains 6 non-human miRNAs:ath-miR159a, cel-miR-2, cel-miR-39, cel-miR-54, cel-miR-238, cel-lin-4.They can be used as external controls at user's choice.

Reagents in the kit: Lysis Buffer, ABC Buffer, Wash Buffer 1, WashBuffer 2, Elution Buffer, LoBind Tubes (Eppendorf), Human Panel A Beads(1 million/microL). Or Human Panel Panel B Beads.

Reagent Preparation: Add 6 mL of Lysis Buffer to the ABC Buffer bottleto make the final ABC Buffer for use. Add 7 mL of 100% Ethanol to theWash Buffer 2 bottle to make the final Wash Buffer 2 for use.

Reagents required: TaqMan® MicroRNA Reverse Transcription Kit (ABI PN:4366597), TaqMan® MicroRNA Assays (ABI PN: 4427975), TaqMan® UniversalMaster Mix II (ABI PN: 4440040)

miRNA Purification

Beads Preparation: Vortex the beads thoroughly to suspend the beads insolution. Sonicate the beads by an ultrasonic water bath for 1 minute.Vortex and then aliquot 80 uL beads (80 million beads total) into aLoBind 1.5-mL microfuge tube. Magnet the beads for 1 minute and removethe supernatant.

Sample Preparation: Select (check mark) the sample type you are going totest. Based on your selection, prepare the sample for hybridizationaccording to following procedures:

Sample Sample Type Amount Preparation Whole  10 uL Mix 10 uL whole bloodwith 20 uL Lysis Buffer and vortex for ^(~)30 Blood seconds. Add 120 uLABC Buffer and vortex for ~30 seconds. Total volume ~150 uL Blood  30 uLDilute 30 uL blood lysate with 120 uL ABC Buffer and vortex. TotalLysate volume ~150 uL Plasma  50 uL Mix 50 uL plasma with 100 uL ABCBuffer and vortex for ~30 seconds. Total volume ~150 uL Serum  50 uL Mix50 uL serum with 100 uL ABC Buffer and vortex for ~30 seconds. Totalvolume ~150 uL Cell 5 × 10{circumflex over ( )}4 Mix the 50 uL cell/PBSsuspension with 150 uL Lysis Buffer and vortex Cultures cells in for ~30seconds. Total volume ~200 uL 50 uL PBS Solid 1-10 mg If needed, grindor homogenize the tissue. Add 30 uL Lysis Buffer and Tissue vortex for~30 seconds. Add 120 uL ABC Buffer and vortex for ~30 seconds. Totalvolume ~150 uL FFPE 1 Wash the FFPE sample with xylene (2 min × 2),100%, 95% and 75% dissection ethanol (1 min each), H₂O (1 min). Add 30uL Lysis Buffer and vortex (5-10 um) for ~30 seconds. Add 120 uL ABCBuffer and vortex for ~30 seconds. Total volume ~150 uL Raw Milk 100 uLMix 100 uL raw milk with 200 uL Lysis Buffer and vortex for ~30 seconds.Total volume ~300 uL Saliva  50 uL Centrifuge 15 min at 2000 rpm toremove debris. Mix 50 uL saliva with 100 uL Lysis Buffer and vortex for~30 seconds. Total volume ~150 uL Urine  50 uL Centrifuge 15 min at 2000rpm to remove debris. Mix 50 uL urine with 100 uL Lysis Buffer andvortex for ~30 seconds. Total volume ~150 uL

(Optional) Spike in 2 uL of 1 nM external control miRNA (following sixcan be captured by the beads: ath-miR-159a, cel-miR-2, cel-miR-39,cel-miR-54, cel-miR-238, cel-Lin4) and vortex.

Hybridization: Transfer all the prepared sample into the bead tubeprepared above. Using a ThermoMixer, shake the vial at 1200 rpm at 30°C. for 40 minutes.

Wash: Magnet the beads for 1 minute and remove the supernatant. Add 100uL Wash Buffer 1. Vortex to resuspend the beads into solution then pulsebriefly. Magnet the beads for 1 minute and remove the supernatant. Add100 uL Wash Buffer 2. Vortex briefly to resuspend the beads intosolution then pulse briefly. Magnet the beads for 1 minute and removethe supernatant. Repeat step c. Pulse the tube down to collect anyresidual liquid. Place the tube on magnetic rack for 20 sec, and removeany residual liquid using a fine pipette tip.

Elution: Add 100 uL Elution Buffer and vortex to mix then pulse briefly.Using a ThermoMixer, shake the tube at 1200 rpm at 70° C. for 3 minutesthen place it immediately on the magnetic stand for 1 minute. Carefullytransfer the supernatant (miRNA sample) into a clean LoBind tube.(Optional—this dilution step is only for a full 96-well plate run. Theconcentrated sample can be directly used). Add 500 uL H₂O to dilute thesample (total volume ^(˜)600 uL). Place the sample vial on ice. Storethe miRNA sample at −80° C. if not used immediately.

Reverse Transcription Reaction

Following operations are for a panel of 96 miRNA assays in a 96-wellplate. Aliquot each 5×RT primer into a 96-well PCR plate, 3 uL per assayper well. Prepare miRNA RT mix:

Volume: Volume: Component Stock 1 Reaction 100 Reactions Nuclease-freedH₂O 4.16 416 25 mM each (100 mM total) 25 mM 0.15 15 dNTPs 50XMultiScribe Reverse 50X 1.0 100 Transcriptase 10X RT Buffer 10X 1.5 15020 U/uL AB RNase Inhibitor 20 U/uL 0.19 19 Total 7.0 700

Pipette 7 uL miRNA RT mix to each well of the RT plate prepared above.Add 5 uL miRNA sample to each well (final total RT volume 15 uL/well).Cover the plate with Heavy-Duty sealing film, mix, and centrifuge.Incubate at 16° C./30 min, 42° C./30 min, 85° C./5 min, 4° C. hold.Store at −20° C.

TAQMAN PCR Reaction

Following operations are for a panel of 96 miRNA assays in a 96-wellplate. Aliquot 20×TaqMan miRNA assays into a 96-well PCR plate, 1 uL perassay per well. Each miRNA assay location should match the correspondingRT plate location. Prepare TaqMan PCR mix.

Volume (uL): Volume (uL): Component Stock 1 reaction 100 reactionNuclease-free dH₂O 7 700 2X Universal Master Mix II 2X 10 1000 Total 171700

Pipette the PCR mix to each well, 17 uL/well. Transfer 2 uL RT reactionsolution obtained from the RT step into corresponding well location ofthe TaqMan plate. Total reaction volume 20 uL. Run PCR: 95° C./10 min,95° C./15 sec & 60° C./60 sec for 40 cycles, Set FAM as reporter dyewith ROX as Reference.

Representative results from various tissues, body fluids, cancer celllines, breast cancer formalin-fixed paraffin-embedded (FFPE) samples,among others are shown in figures XX-XX and tables below. The miRNAs areisolated from various tissues using Laser Capture Microdissection (LCM)technique.

miRNA profiling from human bladder LCM samples

hsa- hsa- hsa- hsa- hsa- LCM Diameter Area, um2 Log(Area) Let-7a Let-7cmiR-16 miR-320 miR-92a NTC 0 40.00 40.00 38.27 37.39 40.00  100 um 78503.8949 35.34 37.56 34.20 35.61 40.00  200 um 31400 4.4969 33.19 35.5231.68 35.50 40.00 1000 um 785000 5.8949 27.16 31.17 28.03 33.28 40.00

Example 9. microRNA Profiling from Urine

The profiling of microRNA in human urine samples during pregnancy atvarious stages of pregnancy showed that of the 384 miRNAs tested, 200were detected in Urine samples using a Ct cutoff of 35. 18 pregnancyrelated miRNAs consistently showed increased expression with pregnancyprogression to second trimester.

Expression of miR143 and miR145 in urine for patients with ballooninjured artery and normal individuals was compared. miR143 and miR145are significantly down regulated in balloon injured arteries incomparison to normal artery. The results are shown in the table below. Arepresentative miRNA profiling is shown in FIG. 17.

Assay ID Workflow Sample ID# Avg. CY StDev Ct miR-143 Indy Normal 35.721.06 miR-143 Indy Stent Artery 48.66 1.9 miR-143 TiLDA Normal 33.08 0.06miR-143 TiLDA Stent Artery 39.61 0.55 miR-145 Indy Normal 36.5 1.63miR-145 Indy Stent Artery 48.09 1.69 miR-145 TiLDA Normal 30.73 0.32miR-145 TiLDA Stent Artery 36.84 0.53

All references cited within this disclosure are hereby incorporated byreference in their entirety. While certain embodiments have beendescribed in terms of the preferred embodiments, it is understood thatvariations and modifications will occur to those skilled in the art.Therefore, it is intended that the appended claims cover all suchequivalent variations that come within the scope of the followingclaims.

1. A method for isolating, identifying, or quantifying an miRNA from a sample of interest, comprising: a) contacting the sample of interest with an anti-miRNA probe covalently attached to a bead; b) incubating the sample of interest—bead mixture under suitable conditions to form hybridized complexes between the miRNA in the sample of interest and the anti-miRNA probes on the beads; c) washing the beads under suitable conditions to remove the unbound sample material; and d) isolating, identifying, or quantifying the miRNA bound to the anti-miRNA probes.
 2. The method according to claim 1, wherein the miRNA is isolated from the anti-miRNA probe beads before identifying or quantifying the miRNA.
 3. The method according to claim 1, wherein the identifying or quantifying the miRNA comprises using reverse transcription followed by real-time (RT) or quantitative polymerase chain reaction (q-PCR).
 4. The method according to claim 1, wherein the beads are magnetic beads.
 5. The method according to claim 4, wherein the beads are carboxylic acid beads.
 6. The method according to claim 4, wherein the beads are DNA beads.
 7. The method according to claim 6, wherein the beads are P1 DNA beads.
 8. The method according to claim 1, wherein the anti-miRNA probe is attached to the beads using chemical synthesis.
 9. The method according to claim 1, wherein the anti-miRNA probe is attached to the beads using enzymatic synthesis.
 10. The method according to claim 9, wherein the enzymatic synthesis comprises: a) taking an oligonucleotide that has a sequence complementary to an miRNA of interest (anti-miRNA probe); b) adding a terminal didexoynucleotide to the 3′ end using a terminal transferase; c) adding a 5′-phosphate group to the oligonucleotide using a kinase; and d) ligating the oligonucleotide to DNA beads using a single-strand DNA ligase.
 11. The method according to claim 1, wherein only one species of anti-miRNA probe is attached to an individual bead.
 12. The method according to claim 1, wherein more than one species of anti-miRNA probes are attached to an individual bead.
 13. The method according to claim 1, wherein the sample of interest is a biological sample.
 14. The method according to claim 13, wherein the biological sample is selected from the group consisting of blood, serum, plasma, urine, saliva, cerebrospinal fluid, wound exudates, biopsies, autopsies, tissues, formalin-fixed, paraffin-embedded (PPFE) samples, and organs.
 15. A method according to claim 14, wherein the biological sample is a biological fluid.
 16. A method according to claim 15, wherein the biological fluid is blood.
 17. A method according to claim 15, wherein the biological fluid is serum.
 18. A method according to claim 15, wherein the biological fluid is saliva.
 19. A method of diagnosing a disease or disease progression, comprising: a) identifying a set of miRNA markers that are differentially regulated during a causation or progression of a disease; b) isolating and measuring the levels of such miRNA markers from a suitable biological sample from a patient in need thereof, at different time points if necessary; and c) diagnosing the disease or its progression over time in the patient.
 20. A kit for isolating, identifying, or quantifying an miRNA from a sample of interest, comprising: a) beads comprising anti-miRNA probe molecules covalently attached thereto; b) a wash buffer; and c) an elution buffer. 